The epidermal growth factor receptor (EGFR, Erb-B1) belongs to a family of proteins, involved in the proliferation of normal and malignant cells (Artega, C. L., J. Clin Oncol 19, 2001, 32-40). Overexpression of Epidermal Growth Factor Receptor (EGFR) is present in at least 70% of human cancers (Seymour, L. K., Curr Drug Targets 2, 2001, 117-133) such as, non-small cell lung carcinomas (NSCLC), breast cancers, gliomas, squamous cell carcinoma of the head and neck, and prostate cancer (Raymond et al., Drugs 60 Suppl 1, 2000, discussion 41-2; Salomon et al., Crit Rev Oncol Hematol 19, 1995, 183-232; Voldborg et al., Ann Oncol 8, 1997, 1197-1206). The EGFR-TK is therefore widely recognized as an attractive target for the design and development of compounds that can specifically bind and inhibit the tyrosine kinase activity and its signal transduction pathway in cancer cells, and thus can serve as either diagnostic or therapeutic agents. For example, the EGFR tyrosine kinase (EGFR-TK) reversible inhibitor, TARCEVA®, is approved by the FDA for treatment of NSCLC and advanced pancreatic cancer. Other anti-EGFR targeted molecules have also been approved including LAPATINIB®, and IRESSA®.
The efficacy of erlotinib and gefitinib is limited when administered to all lung cancer patients. When erlotinib or gefitinib are used in the treatment of all lung cancer patients (not selected for presence/absence of activated (mutant) EGFR), the likelihood of tumor shrinkage (response rate) is 8-10% and the median time to tumor progression is approximately 2 months {Shepherd et al NEJM 2004, Thatcher et al. Lancet 2005}. In 2004 it was discovered that lung cancers with somatic mutations in EGFR were associated with dramatic clinical responses following treatment with geftinib and erlotinib {Paez et al. Science 2004; Lynch et al. NEJM 2004; Pao et al PNAS 2004}. Somatic mutations identified to date include point mutations in which a single aminoacid residue is altered in the expressed protein (e.g. L858R, G719S, G719C, G719A, L861Q), as well as small in frame deletions in Exon19 or insertions in Exon20. Somatic mutations in EGFR are found in 10-15% of Caucasian and in 30-40% of Asian NSCLC patients. EGFR mutations are present more frequently in never-smokers, females, those with adenocarcinoma and in patients of East Asian ethnicity {Shigematsu et al JNCI 2005}. These are the same groups of patients previously clinically identified as most likely to benefit from gefltinib or erlotinib {Fukuoka et al. JCO 2003; Kris et al JAMA 2003 and Shepherd et al NEJM 2004}. Six prospective clinical trials treating chemotherapy na[iota]ve patients with EGFR mutations with gefltinib or erlotinib have been reported to date {Inoue et al JCO 2006, Tamura et al Br. J Cancer 2008; Asahina et al., Br. J. Cancer 2006; Sequist et al., JCO 2008}. Cumulatively, these studies have prospectively identified and treated over 200 patients with EGFR mutations. Together they demonstrate radiographic response rates ranging from 60-82% and median times to progression of 9.4 to 13.3 months in the patients treated with gefltinib and erlotinib. These outcomes are 3 to 4 folder greater than that observed with platin-based chemotherapy (20-30% and 3-4 months, respectively) for advanced NSCLC {Schiller, et al JCO 2002}. In a recently completed phase III clinical trial, EGFR mutant chemotherapy na[iota]ve NSCLC patients had a significantly longer (hazard ratio=0.48 (95% CI; 0.36-0.64); p<0.0001) progression free survival (PFS) and tumor response rate (71.3 vs. 47.2%; p=0.0001) when treated with gefltinib compared with conventional chemotherapy {Mok et al. ESMO meeting 2008}. Conversely, NSCLC patients that were EGFR wild type had a worse outcome when they received gefltinib compared to chemotherapy as their initial treatment for advanced NSCLC {Mok et al ESMO meeting 2008}. Thus EGFR mutations provide an important selection method for NSCLC patients for a therapy (EGFR TKIs) that is more effective than conventional systemic chemotherapy. EGFR mutations are routinely being evaluated in NSCLC patients in many clinical centers.
Despite the initial clinical benefits of gefitinib/erlotinib in NSCLC patients harboring EGFR mutations, most if not all patients ultimately develop progressive cancer while receiving therapy on these agents. Initial studies of relapsed specimens identified a secondary EGFR mutation, T790M, that renders gefitinib and erlotinib ineffective inhibitors of EGFR kinase activity {Kobayashi et al NEJM 2005 and Pao et al PLOS Medicien 2005}. Subsequent studies have demonstrated that the EGFR T790M mutation is found in approximately 50% of tumors (24/48) from patients that have developed acquired resistance to gefitinib or erlotinib {Kosaka et al CCR 2006; Balak et al CCR 2006 and Engelman et al Science 2007}. This secondary genetic alteration occurs in the ‘gatekeeper’ residue and in an analogous position to other secondary resistance alleles in diseases treated with kinase inhibitors (for example T315I in ABL in imatinib resistant CML).
The initial identification of EGFR T790M also determined that an irreversible EGFR inhibitor, CL-387,785, could still inhibit EGFR even when it possessed the T790M mutation. Subsequent studies demonstrated that other irreversible EGFR inhibitors, EKB-569 and HKI-272, could also inhibit phosphorylation of EGFR T790M and the growth of EGFR mutant NSCLC cell lines harboring the T790M mutation {Kwak et al PNAS 2005; Kobayashi et al NEJM 2005}. These irreversible EGFR inhibitors are structurally similar to reversible inhibitors gefitinib and erlotinib, but differ in that they contain a Michael-acceptor that allows them to covalently bind EGFR at Cys 797. The T790M mutation does not preclude binding of irreversible inhibitors; instead, it confers resistance to reversible inhibitors in part by increasing the affinity of the enzyme for ATP, at least in the L858R/T790M mutant EGFR {Yun et al., PNAS 2008}. Irreversible inhibitors overcome this mechanism of resistance because once they are covalently bound, they are no longer in competition with ATP. These observations have led to clinical development of irreversible EGFR inhibitors for patients developing acquired resistance to gefitinib or erlotinib. Three such agents (HKI-272, BIBW2992 and PF00299804) are currently under clinical development. However, the preclinical studies to date would suggest that these agents are not optimal at inhibiting EGFR variants bearing the T790M mutation.
Recent studies in a mouse model of EGFR L858R/T790M mediated lung cancer demonstrate that a subset of cancers in these mice (bronchial tumors) were insensitive to HKI-272 alone {Li et al Cancer Cell 2007}. Thus even in this solely EGFR-driven model, HKI-272 alone is unable to cause tumor regression. This is in sharp contrast to the dramatic effects of erlotinib alone in mouse lung cancer models that contain only EGFR activating mutations {Ji et al Cancer Cell 2006} and suggests that HKI-272 may also be ineffective in some NSCLC patients with EGFR T790M. Similar findings have been reported for BIBW 2992 (Li et al. Oncogene 2008) Furthermore, the IC50 of HKI-272 required to inhibit the growth of Ba/F3 cells harboring EGFR T790M in conjunction with different exon 19 deletion mutations ranges from 200-800 nM while the mean Cmax in the Phase I trial was only about 200 nM {Yuza et al Cancer Biol Ther 2007; Wong et al CCR 2009 in press}. Thus there continues to be a need to develop more effective EGFR targeted agents capable of inhibiting EGFR T790M.
A major limitation of all current EGFR inhibitors is the development of toxicity in normal tissues. Since ATP affinity of EGFR T790M is similar to WT EGFR, the concentration of an irreversible EGFR inhibitor required to inhibit EGFR T790M will also effectively inhibit WT EGFR. The class-specific toxicities of current EGFR kinase inhibitors, skin rash and diarrhea, are a result of inhibiting WT EGFR in non-cancer tissues. This toxicity, as a result of inhibiting WT EGFR, precludes dose escalation of current agents to plasma levels that would effectively inhibit EGFR T790M. A major advance would be the identification of a mutant specific EGFR inhibitor that was less effective against wild type EGFR. Such an agent would likely be clinically more effective and also potentially more tolerable as a therapeutic agent in patients with cancer.
Anaplastic lymphoma kinase (ALK) belongs to the receptor tyrosine kinase (RTK) superfamily of protein kinases. ALK expression in normal adult human tissues is restricted to endothelial cells, pericytes, and rare neural cells. Oncogenic, constitutively active ALK fusion proteins are expressed in anaplastic large cell lymphoma (ALCL) and inflammatory myofibroblastic tumors (IMT). ALK has also recently been implicated as an oncogene in a small fraction of non-small-cell lung cancers and neuroblastomas (Choi et al, Cancer Res 2008; 68: (13); Webb et al, Expert Rev. Anticancer Ther. 9(3), 331-356, 2009).
Anaplastic large-cell lymphomas (ALCLs) are a subtype of the high-grade non-Hodgkin's family of lymphomas with distinct morphology, immunophenotype, and prognosis. ALCLs are postulated to arise from T cells and, in rare cases, can also exhibit a B cell phenotype. In addition, there are 40% of cases for which the cell of origin remains unknown and that are classified as “null”. First described as a histological entity by Stein et al. based on the expression of CD30 (Ki-1), ALCL presents as a systemic disease afflicting skin, bone, soft tissues, and other organs, with or without the involvement of lymph nodes. ALCL can be subdivided into at least two subtypes, characterized by the presence or absence of chromosomal rearrangements between the anaplastic lymphoma kinase (ALK) gene locus and various fusion partners such as nucleophosmin (NPM). Approximately 50-60% of cases of ALCL are associated with the t(2;5)(p23; q35) chromosomal translocation, which generates a hybrid gene consisting of the intracellular domain of the ALK tyrosine kinase receptor juxtaposed with NPM. The resulting fusion protein, NPM-ALK has constitutive tyrosine kinase activity and has been shown to transform various hematopoietic cell types in vitro and support tumor formation in vivo.
NPM-ALK, an oncogenic fusion protein variant of the Anaplastic Lymphoma Kinase, which results from a chromosomal translocation is implicated in the pathogenesis of human anaplastic large cell lymphoma (Pulford K, Morris S W, Turturro F. Anaplastic lymphoma kinase proteins in growth control and cancer. J Cell Physiol 2004; 199: 330-58). The roles of aberrant expression of constitutively active ALK chimeric proteins in the pathogenesis of ALCL have been well defined (Weihua Wan, et. al. Anaplastic lymphoma kinase activity is essential for the proliferation and survival of anaplastic large cell lymphoma cells. Blood First Edition Paper, prepublished online Oct. 27, 2005; DOI 10.1182/blood-2005-08-3254). NPM-ALK is implicated in the dysregulation of cell proliferation and apoptosis in ALCL lymphoma cells (Pulford et al, 2004).
Other less frequent ALK fusion partners, e.g., tropomyosin-3 and clathrin heavy chain, have also been identified in ALCL as well as in CD30-negative diffuse large-cell lymphoma. Despite subtle differences in signaling and some biological functions, all fusions appear to be transforming to fibroblasts and hematopoietic cells. Extensive analysis of the leukemogenic potential of NPM-ALK in animal models has further corroborated the importance of NPM-ALK and other ALK rearrangements in the development of ALK-positive ALCL and other diseases.
ALK fusion proteins have also been detected in cell lines and/or primary specimens representing a variety of other tumors including inflammatory myofibroblastic tumor (IMT), neuroectodermal tumors, glioblastomas, melanoma, rhabdomyosarcoma tumors, and esophageal squamous cell carcinomas (see review by Webb T R, Slavish J, et al. Anaplastic lymphoma kinase: role in cancer pathogenesis and small-molecule inhibitor development for therapy. Expert Rev Anticancer Ther. 2009; 9(3): 331-356). Recently, ALK is also implicated in small percent of breast colorectal and non-small cell lung cancers (Lin E, Li L, et al. Exon Array Profiling Detects EML4-ALK Fusion in Breast, Colorectal, and Non-Small Cell Lung Cancers. Mol Cancer Res 2009; 7(9): 1466-76).
Approximately 3-7% of lung tumors harbor ALK fusions, and multiple different ALK rearrangements have been described in NSCLC. The majority of these ALK fusion variants are comprised of portions of the echinoderm microtubule-associated protein-like 4 (EML4) gene with the ALK gene. At least nine different EML4-ALK fusion variants have been identified in NSCLC (Takeuchi et al. Multiplex reverse transcription-PCR screening for EML4-ALK fusion transcripts. Clin Cancer Res. 2008, 15(9):3143-9). In addition, non-EML4 fusion partners have also been identified, including KIFSB-ALK (Takeuchi et al. KIFSB-ALK, a novel fusion oncokinase identified by an immunohistochemistry-based diagnostic system for ALK-positive lung cancer. 2009, 15(9):3143-9) and TFG-ALK (Rikova et al. Global survey of phosphotyrosine signaling identifies oncogenic kinases in lung cancer. Cell 2007, 131(6):1190-203).
The various N-terminal fusion partners promote dimerization and therefore constitutive kinase activity. Signaling downstream of ALK fusions results in activation of cellular pathways known to be involved in cell growth and cell proliferation (Mosse et al. Inhibition of ALK signaling for cancer therapy. Clin Cancer Res. 2009, 15(18):5609-14).